How to fix attributeError: module 'scvi' has no attribute 'model'?

Question

[Chris]

Hi all,

I try to follow the tutorial below and get an error.

https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb

Many people got the same error but the solution doesn't work in my case:

https://github.com/scverse/scvi-tools/issues/824

scvi.model.SCVI.setup_anndata(adata)

vae = scvi.model.SCVI(adata)

vae.train()

--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-10-246da2622341> in <module>

----> 1 scvi.model.SCVI.setup_anndata(adata)

2 vae = scvi.model.SCVI(adata)

3 vae.train()

AttributeError: module 'scvi' has no attribute 'model'

What is wrong in my case? Thank you so much!

Update. I figured it out.

[Andy]

I meet exact same error, could you please share how you solved the problem?

[Chris]

It was a long time ago so I am not sure what I did. Try to uninstall the package and reinstall it.

[Andy]

Yeah, it is. I solved the problem too. I think the problem is because I use pip install SCVI, but I actually need to pip instal SCVI-tools.

[Chris]

So the command pip install SCVI is not correct? Glad that you can fix the error.

[Andy]

Yes, you are correct. The author has stopped maintaining SCVI for a long time. We should use SCVI-tools instead.

[Chris]

Thanks for the info.